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Sebastian Doniach

Sebastian Doniach
Professor of Applied Physics and of Physics, Emeritus
Department:
Applied Physics
Ph.D., University of Liverpool, England, Physics (1958)
B.A., Cambridge University, England, Physics (1954)
How is the function of biomolecules in living systems related to their atomic structure?

Professor Doniach's research group uses scattering of synchotron X-rays from electron storage rings at SLAC and at the Argonne National Laboratory to study changes in the conformation of molecules as their solvent environments are changed. The research also involves computer simulations of the dynamics and energetic of the resulting changes.

recent Advances in the biology of DNA have shown that a very large part of the genome in eukaryotes codes for small RNA molecules that appear to be centralto the way the genes (coding for proteins) are put together. Doniach's group is currently studying structural changes that occur when some small functional RNA's turn on and off gene expression (riboswitches) without needing to involve protein transcription factors. Understanding RNA control mechanisms is central to our ability to intervene in biological functions such as generation of biofuels by bacteria or of intervention when cells start to go cancerous.

The Doniach group's bio-simulation work involves new ways to represent changes in molecular structure, in which the entire trajectory for a change of conformation is represented in a large number of CPU's where each time slice of the trajectory is managed by one of the CPU's. In this way, a representationof changes involving thousands of degrees of freedom may be obtained at atomic reslution. This method has recently been applied to look at protein misfolding. Another project involves using a highly simplified normal mode representationto represent large scale conformational changes in molecular motor molecules and DNS polymerase.

The group is also working on ways to improve the methods of computing the statistical mechanics of counter-ion shielding of the very large Coulomb forces endangered by the phosphate backbones of DNA and RNA. Software has been developed that modifies the solving of the Poisson Boltzmann equation to include the effects of finite ion size. Further modifications are being worked in to include effects of ion-on correlations.

Current Area of Focus:
- Membrane Proteins

Publications

Bhatkar, S., Ma, M., Zsolway, M., Tarafder, A., Doniach, S., & Bhanot, G. (2023). Asymmetry in the peak in Covid-19 daily cases and the pandemic R-parameter. MedRxiv : the Preprint Server for Health Sciences.
2023
Jung, J. H., Reist, N. E., & Doniach, S. (2023). Editorial: Structural and quantitative modeling of synapses. Frontiers in Synaptic Neuroscience, 15, 1254416.
2023
Raines, K. S., Doniach, S., & Bhanot, G. (2021). The transmission of SARS-CoV-2 is likely comodulated by temperature and by relative humidity. PloS One, 16(7), e0255212.
2021
Panda, A., Yadav, A., Yeerna, H., Singh, A., Biehl, M., Lux, M., … Bhanot, G. (2020). The composition of the human ribosome varies significantly in different normal and malignant tissues. CANCER RESEARCH. AMER ASSOC CANCER RESEARCH.
2020
Panda, A., Yadav, A., Yeerna, H., Singh, A., Biehl, M., Lux, M., … Bhanot, G. (2020). Tissue- and development-stage-specific mRNA and heterogeneous CNV signatures of human ribosomal proteins in normal and cancer samples. Nucleic Acids Research.
2020
Jung, J. H., & Doniach, S. (2017). A stochastic model of active zone material mediated synaptic vesicle docking and priming at resting active zones. SCIENTIFIC REPORTS, 7, 278.
2017
Matsuura, A. Y., Watanabe, K., Kim, C., Doniach, S., Shen, Z. X., Thio, T., & Bennett, J. W. (1998). Metal-insulator transition in NiS2-xSex and the local impurity self-consistent approximation model. PHYSICAL REVIEW B, 58(7), 3690–3696.
1998
Doniach, S. (1996). Phase diagram was out of Sync with record. PHYSICS TODAY, 49(9), 117-&.
1996
Onogi, T., & Doniach, S. (1996). Simulation of quantum melting of the vortex lattice and of fractional quantum Hall-like states of the quantum vortex liquid in 2D superconductors. SOLID STATE COMMUNICATIONS, 98(1), 1–5.
1996
Doniach, S. (1995). Reflections on the superconductor insulator transition. JOURNAL OF PHYSICS AND CHEMISTRY OF SOLIDS. PERGAMON-ELSEVIER SCIENCE LTD.
1995
DONIACH, S., FU, C., & TRUGMAN, S. A. (1994). KONDO INSULATORS - ARE SIMPLE THEORIES GOOD ENOUGH. PHYSICA B. ELSEVIER SCIENCE BV.
1994
HUI, A., & DONIACH, S. (1993). PENSON-KOLB-HUBBARD MODEL - A STUDY OF THE COMPETITION BETWEEN SINGLE-PARTICLE AND PAIR HOPPING IN ONE-DIMENSION. PHYSICAL REVIEW B, 48(4), 2063–2073.
1993
SADEMELO, C. A., WANG, Z. Q., & DONIACH, S. (1992). FERMI-LIQUID PHASE OF THE T-J MODEL AND THE HALL-COEFFICIENT IN HIGH-TEMPERATURE SUPERCONDUCTORS. PHYSICAL REVIEW LETTERS, 68(13), 2078–2081.
1992
DONIACH, S. (1992). THE READERS NIH. SCIENCE, 258(5082), 531.
1992
DONIACH, S., & FAZEKAS, P. (1992). MAGNETISM IN DOPED KONDO INSULATORS. PHILOSOPHICAL MAGAZINE B-PHYSICS OF CONDENSED MATTER STATISTICAL MECHANICS ELECTRONIC OPTICAL AND MAGNETIC PROPERTIES, 65(6), 1171–1183.
1992
SOMMERS, C., DONIACH, S., & FU, C. (1991). A NEW APPROACH TO A NONLOCAL DENSITY FUNCTIONAL FOR THE CALCULATION OF ELECTRON CORRELATION ENERGIES. PHYSICA B. ELSEVIER SCIENCE BV.
1991
CECCATTO, A., DONIACH, S., FRAHM, K., & MUHLSCHLEGEL, B. (1991). THE NATURE OF THE FLUX LATTICE IN ANTIGRANULOCYTES SUPERCONDUCTING NETWORKS. ZEITSCHRIFT FUR PHYSIK B-CONDENSED MATTER, 82(2), 257–265.
1991
INUI, M., DONIACH, S., HIRSCHFELD, P. J., & RUCKENSTEIN, A. E. (1988). COEXISTENCE OF ANTIFERROMAGNETISM AND SUPERCONDUCTIVITY IN A MEAN-FIELD THEORY OF HIGH-TC SUPERCONDUCTORS. PHYSICAL REVIEW B, 37(4), 2320–2323.
1988
CZYCHOLL, G., & DONIACH, S. (1985). A BCS THEORY FOR HEAVY FERMION SUPERCONDUCTIVITY. JOURNAL OF MAGNETISM AND MAGNETIC MATERIALS, 47-8(FEB), 17–19.
1985
STRENSKI, P. N., & DONIACH, S. (1985). A SYSTEM OF 3 JOSEPHSON-JUNCTIONS. JOURNAL OF APPLIED PHYSICS, 57(3), 867–874.
1985
GELBAND, P., & DONIACH, S. (1985). THERMODYNAMICS OF MONOLAYER FORMATION ON AN IMPURE SUBSTRATE - RANDOM-FIELD ISING-MODEL APPROACH. PHYSICAL REVIEW B, 31(7), 4361–4368.
1985
KUTZLER, F. W., HODGSON, K. O., & DONIACH, S. (1982). K-EDGE X-RAY ABSORPTION-SPECTRA IN AN OCTAHEDRAL ENVIRONMENT - A THEORETICAL AND EXPERIMENTAL-STUDY OF MO(CO)6. PHYSICAL REVIEW A, 26(5), 3020–3022.
1982
HUBERMAN, B. A., & DONIACH, S. (1979). MELTING OF 2-DIMENSIONAL VORTEX LATTICES. PHYSICAL REVIEW LETTERS, 43(13), 950–952.
1979
CAILLE, A., RAPINI, A., ZUCKERMANN, M. J., CROS, A., & DONIACH, S. (1978). SIMPLE-MODEL FOR PHASE-TRANSITIONS IN MONOLAYERS AND BILAYERS OF LIPID MOLECULES. CANADIAN JOURNAL OF PHYSICS, 56(3), 348–357.
1978
JULLIEN, R., FIELDS, J. N., & DONIACH, S. (1977). ZERO-TEMPERATURE REAL-SPACE RENORMALIZATION-GROUP METHOD FOR A KONDO-LATTICE MODEL HAMILTONIAN. PHYSICAL REVIEW B, 16(11), 4889–4900.
1977
DONIACH, S. (1973). THEORY OF CRITICAL-TEMPERATURE OF SUPERFLUID PHASE-TRANSITIONS IN 2 DIMENSIONS. PHYSICAL REVIEW LETTERS, 31(24), 1450–1453.
1973
MURATA, K. K., & DONIACH, S. (1972). THEORY OF MAGNETIC FLUCTUATIONS IN ITINERANT FERROMAGNETS. PHYSICAL REVIEW LETTERS, 29(5), 285-&.
1972
DONIACH, S., ROULET, B. J., & FISHER, M. E. (1971). EXCITONS IN MOTT-HUBBARD INSULATORS. PHYSICAL REVIEW LETTERS, 27(5), 262-&.
1971

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